Contacts of the helix formed by residues 259 - 269 (chain J) in PDB entry 3SWD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 259 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232J ARG* 3.7 33.9 - - + +
235J THR* 3.6 32.8 - - + -
236J GLY* 4.4 4.3 - - - +
239J LEU* 4.8 5.8 - - + -
255J GLN 5.4 0.9 - - - +
256J PRO 2.8 11.5 + - - +
258J THR* 1.3 91.1 - - + +
260J ASP* 1.3 67.5 + - - +
261J ALA 3.6 1.1 - - - -
262J VAL* 3.2 37.0 + - + -
263J LEU* 2.9 31.7 + - + +
280J ILE* 4.2 11.2 - - + -
303J PRO* 5.7 2.5 - - + -
306J MET* 5.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 260 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256J PRO 3.9 2.1 - - - +
257J ASP* 3.4 30.5 - - - +
258J THR 3.7 1.8 + - - -
259J LEU* 1.3 76.7 - - - +
261J ALA* 1.3 63.8 + - - +
263J LEU* 3.6 4.3 - - - +
264J ALA* 3.0 21.4 + - - +
299J HIS* 5.7 3.0 + - - -
300J PRO* 4.8 16.4 + - + +
155K HIS* 4.9 9.2 - - + -
157K VAL* 4.6 20.1 - - + +
183K GLU* 3.9 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 261 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259J LEU 3.6 0.2 - - - -
260J ASP* 1.3 76.3 - - - +
262J VAL* 1.3 62.0 + - - +
264J ALA* 3.7 0.9 + - - +
265J LYS* 3.1 29.9 + - + +
300J PRO 3.4 16.8 + - - +
301J ALA* 3.7 1.8 - - - +
302J PHE* 3.3 40.7 - - + +
303J PRO* 5.2 1.1 - - + -
157K VAL* 4.0 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236J GLY* 4.8 11.7 - - - -
239J LEU* 5.2 0.4 - - + -
259J LEU* 3.2 38.3 + - + +
260J ASP 3.1 1.0 - - - -
261J ALA* 1.3 74.5 - - + +
263J LEU* 1.3 71.3 + - + +
265J LYS* 2.8 15.2 + - - +
266J LEU* 2.9 32.7 + - + +
302J PHE* 4.6 11.4 - - + -
303J PRO* 4.1 24.0 - - + -
306J MET* 4.4 11.0 - - + -
310J PHE* 4.0 13.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239J LEU* 4.1 27.1 - - + -
256J PRO* 4.3 8.5 - - + +
259J LEU* 2.9 31.8 + - + +
260J ASP* 3.8 3.8 - - - +
262J VAL* 1.3 75.4 - - + +
264J ALA* 1.3 62.8 + - - +
266J LEU* 3.3 6.2 + - + -
267J ARG* 3.1 44.4 + - - +
273J ILE* 3.5 23.4 - - + +
275J VAL* 4.6 16.4 - - + -
280J ILE* 4.2 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260J ASP 3.0 15.5 + - - +
261J ALA 4.0 3.4 - - - +
263J LEU* 1.3 74.9 - - - +
265J LYS* 1.3 69.5 + - + +
267J ARG* 3.2 16.8 + - - +
268J ASP* 3.2 27.9 + - - +
157K VAL* 4.0 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 265 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261J ALA* 3.1 20.5 + - + +
262J VAL 2.8 9.4 + - - +
264J ALA* 1.3 76.7 - - + +
266J LEU* 1.3 61.9 + - - +
268J ASP* 3.1 29.9 + - - +
269J ALA* 3.1 20.4 + - - +
292J VAL* 4.3 10.5 - - + +
293J ASN* 2.7 33.3 + - - +
294J VAL* 4.0 23.2 - - + +
302J PHE* 4.5 11.2 - - + -
310J PHE* 4.1 17.7 - - + -
157K VAL* 6.1 0.7 - - + -
159K ASP* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 266 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239J LEU* 4.2 27.4 - - + -
240J VAL* 4.6 7.2 - - + -
243J ALA* 4.1 25.6 - - + -
262J VAL* 2.9 32.6 + - + +
263J LEU* 3.5 13.0 - - + +
265J LYS* 1.3 77.7 - - - +
267J ARG* 1.3 57.3 + - - +
269J ALA* 2.9 23.4 - - + +
271J ALA* 3.2 21.6 + - + +
273J ILE* 4.1 9.2 - - + -
282J LEU* 4.5 7.9 - - + -
310J PHE* 3.6 25.6 - - + -
313J LEU* 4.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263J LEU* 3.1 37.5 + - - +
264J ALA* 3.7 13.0 - - - +
265J LYS 3.2 0.6 - - - -
266J LEU* 1.3 71.5 - - - +
268J ASP* 1.3 55.3 + - - +
269J ALA 2.8 5.2 - - - -
270J GLY* 2.5 29.5 + - - -
271J ALA 4.1 13.0 - - - +
273J ILE* 3.7 44.5 + - + +
275J VAL* 5.4 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 268 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264J ALA* 3.2 14.2 + - - +
265J LYS* 3.1 35.8 + - - +
267J ARG* 1.3 75.2 - - - +
269J ALA* 1.3 59.9 + - - +
270J GLY* 3.2 0.9 + - - -
290J LYS* 4.3 9.0 - - - +
292J VAL* 3.6 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 269 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265J LYS 3.1 11.2 + - - +
266J LEU* 2.9 20.4 - - + +
267J ARG 2.8 0.2 + - - -
268J ASP* 1.3 78.2 - - - +
270J GLY* 1.3 56.1 + - - +
271J ALA* 3.6 1.8 - - + +
284J MET* 4.4 1.7 - - + +
289J PRO* 3.3 20.0 - - + +
290J LYS* 2.9 44.7 + - - +
292J VAL* 3.8 4.7 - - + +
310J PHE* 5.8 0.7 - - + -
313J LEU* 4.7 15.0 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il